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Genome-wide Analysis of Chromatin St...

Winter, Deborah Rachelle.

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Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types./
Author:	Winter, Deborah Rachelle.
Description:	211 p.
Notes:	Source: Dissertation Abstracts International, Volume: 74-08(E), Section: B.
Contained By:	Dissertation Abstracts International74-08B(E).
Subject:	Biology, Bioinformatics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3558843
ISBN:	9781303034589

Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types.
Winter, Deborah Rachelle.

Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types. - 211 p.

Source: Dissertation Abstracts International, Volume: 74-08(E), Section: B.

Thesis (Ph.D.)--Duke University, 2013.

Chromatin structure plays an important role in gene regulation, especially in differentiating the diverse cell types in humans. In this dissertation, we analyze the nucleosome positioning and open chromatin profiles genome-wide and investigate the relationship with transcription initiation, the activity of regulatory elements, and expression levels. We mainly focus on the results of DNase-seq experiments, but also employ annotations from MNase-seq, FAIRE-seq, ChIP-seq, CAGE, and RNA microarrays. Our methods are based on computational approaches including managing large data sets, statistical analysis, and machine learning. We find that different transcription initiation patterns lead to distinct chromatin structures, suggesting diverse regulatory strategies. Moreover, we present a tool for comparing genome-wide annotation tracks and evaluate DNase-seq against a unique assay for detecting open chromatin. We also demonstrate how DNase-seq can be used to successfully predict rotationally stable nucleosomes that are conserved across cell types. We conclude that DNase-seq can be used to study genome-wide chromatin structure in an effort to better understand how it regulates gene expression.

ISBN: 9781303034589Subjects--Topical Terms:

1018415
Biology, Bioinformatics.

Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types.
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520 $a Chromatin structure plays an important role in gene regulation, especially in differentiating the diverse cell types in humans. In this dissertation, we analyze the nucleosome positioning and open chromatin profiles genome-wide and investigate the relationship with transcription initiation, the activity of regulatory elements, and expression levels. We mainly focus on the results of DNase-seq experiments, but also employ annotations from MNase-seq, FAIRE-seq, ChIP-seq, CAGE, and RNA microarrays. Our methods are based on computational approaches including managing large data sets, statistical analysis, and machine learning. We find that different transcription initiation patterns lead to distinct chromatin structures, suggesting diverse regulatory strategies. Moreover, we present a tool for comparing genome-wide annotation tracks and evaluate DNase-seq against a unique assay for detecting open chromatin. We also demonstrate how DNase-seq can be used to successfully predict rotationally stable nucleosomes that are conserved across cell types. We conclude that DNase-seq can be used to study genome-wide chromatin structure in an effort to better understand how it regulates gene expression.
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